To study the safety and efficacy of a new medical food (Theramine) in the treatment of low back pain, we performed a 28-day double-blind randomized controlled trial in 129 patients. Back pain was present for at least 6 weeks and was not mild. Patients were randomly assigned to receive medical food alone (n = 43), naproxen alone (250 mg/d, n = 42), or both medical food and naproxen (n = 44). All patients were assessed by using Roland-Morris Disability Questionnaire, Oswestry Low Back Pain Scale, Visual Analog Scale Evaluation and laboratory analysis performed at baseline and at 28 days for assessing the safety and impact on inflammatory markers, which included complete blood counts, C-Reactive protein (CRP), and liver function (alkaline phosphatase, aspartate transaminase, and alanine transaminase). At baseline, there were no statistically significant differences in low back pain when assessed by Roland-Morris function or Oswestry assessments nor were there differences in the blood indices of inflammation. At day 28, both the medical food group and combined therapy group (medical food with naproxen) were statistically significantly superior to the naproxen-alone group (P < 0.05). The medical food and naproxen group showed functional improvement when compared to the naproxen-alone group. The naproxen-alone group showed significant elevations in CRP, alanine transaminase, and aspartate transaminase when compared with the other groups. Medical food alone or with naproxen showed no significant change in liver function tests or CRP, with medical food potentially mitigating the effects seen with naproxen alone. The medical food (Theramine) appeared to be effective in relieving back pain without causing any significant side effects and may provide a safe alternative to presently available therapies.